Calculating   accurate   2D PROTEIN  structures   from   nucleotide sequences  

Info

3D  in  development

Benefits for data interpretation

Source data taken from X-ray diffraction and NMR :

1) Obtained from a two-dimensional image of a three-dimensional object.

2) They do not distinguish fragments of fundamental  (Alpha, Beta, Pi, 310)  helices in the protein structure, 

super secondary helices from fundamental helices, right-handed helices from left-handed helices etc.

3) The error along the 1D structure is plus or minus 5 amino acid residues.

4) The length of "invisible tails" in experiments is 30-50 amino acid residues.

5) There is virtually zero certainty for 97% of proteins that do not crystallize, so there is not enough data for training AI.

We have solved the problem of how to eliminate the difficulties of interpreting X-ray diffraction and NMR data

The 2D PicoTech program is capable of calculating an average of 6 million accurate 2D structures per hour from nucleotide sequences entered in the  .fasta and  .fa formats.

PicoTechnology of proteins method description. 

The strong correlation dependence of spatial structure of the protein from its nucleotide sequence was theoretically predicted by physical modelling, experimentally  discovered and statistically confirmed. In the process of biosynthesis the third nucleotide of the codon controls the orientation of the amino acid forming the concrete spatial isomer that is the conformation of the protein molecule cutting off competition ways of the forming of 2D and 3D structures. On this base the computer program 2D PicoTech program for the calculation of 2D structure of the proteins on their nucleotide sequence was created. 

Within our Protein PicoTechnology method:

- All amino acids can be represented as ring-shaped polyhedral spatial structures. 

- This allows the protein chain to be constructed using a spatial algorithm: 

1) for 2D structures – a compositional genetic code (using programmable compositional angles corresponding to the assembly angles of fundamerntal Alpha, Beta, Pi, and 310 helices); 

2) for 3D structures – with corrections in the form of "non-programmable" second-order angles, which are taken into account (transposition angles, Proline angles, transition angles between helices, the Methionine algorithm,  others).

- 2D structure calculation is accurate and automated.

- The 2D Protein Picotechnology diagrams display using color identification all types of helical regions of the protein chain, individual turns, and single amino acid residues in accordance with their compositional code.

- The third letter of the triplet controls the rotation angle of the next amino acid residue relative to the previous one.

- A 3D Genetic Code table for 2D structure calculation has been published.

- Programs for 3D structures calculation are in development.

We  are  confident  that  it  works !